Usually, I represent this with a long-form GRanges with a sample column. But there is no formal notion of sample, and sample-level data needs to be "denormalized".
I think you are asking for something similar to GenomicFileViews, except for GRanges instead of files. An implementation might be a GenomicRangesList, except the Seqinfo is coordinated across all elements. The mcols() on the GRL would hold the phenotype data. On Wed, Aug 12, 2015 at 2:01 PM, Vincent Carey <[email protected]> wrote: > It seems to me we may need a class to manage related annotation > structures. For example, the chromImpute segmentations of the genome > defined for various cell types. I would like to be able to take a region > of the genome (say a SNP) and ask how the state varies across cell types. > > AnnotationHub will provide access to cell-type specific GRanges but there > is no container that I can think of that would coordinate these as > analogous > to different "samples". > > Am I missing something? > > [[alternative HTML version deleted]] > > _______________________________________________ > [email protected] mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > [[alternative HTML version deleted]] _______________________________________________ [email protected] mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
